1171 lines
41 KiB
Python
1171 lines
41 KiB
Python
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# -*- coding: utf-8 -*-
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"""
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Sphinx directive to support embedded yap_ipython code.
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This directive allows pasting of entire interactive yap_ipython sessions, prompts
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and all, and their code will actually get re-executed at doc build time, with
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all prompts renumbered sequentially. It also allows you to input code as a pure
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python input by giving the argument python to the directive. The output looks
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like an interactive ipython section.
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To enable this directive, simply list it in your Sphinx ``conf.py`` file
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(making sure the directory where you placed it is visible to sphinx, as is
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needed for all Sphinx directives). For example, to enable syntax highlighting
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and the yap_ipython directive::
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extensions = ['yap_ipython.sphinxext.ipython_console_highlighting',
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'yap_ipython.sphinxext.ipython_directive']
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The yap_ipython directive outputs code-blocks with the language 'ipython'. So
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if you do not have the syntax highlighting extension enabled as well, then
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all rendered code-blocks will be uncolored. By default this directive assumes
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that your prompts are unchanged yap_ipython ones, but this can be customized.
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The configurable options that can be placed in conf.py are:
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ipython_savefig_dir:
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The directory in which to save the figures. This is relative to the
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Sphinx source directory. The default is `html_static_path`.
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ipython_rgxin:
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The compiled regular expression to denote the start of yap_ipython input
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lines. The default is re.compile('In \[(\d+)\]:\s?(.*)\s*'). You
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shouldn't need to change this.
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ipython_rgxout:
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The compiled regular expression to denote the start of yap_ipython output
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lines. The default is re.compile('Out\[(\d+)\]:\s?(.*)\s*'). You
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shouldn't need to change this.
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ipython_promptin:
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The string to represent the yap_ipython input prompt in the generated ReST.
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The default is 'In [%d]:'. This expects that the line numbers are used
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in the prompt.
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ipython_promptout:
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The string to represent the yap_ipython prompt in the generated ReST. The
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default is 'Out [%d]:'. This expects that the line numbers are used
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in the prompt.
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ipython_mplbackend:
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The string which specifies if the embedded Sphinx shell should import
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Matplotlib and set the backend. The value specifies a backend that is
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passed to `matplotlib.use()` before any lines in `ipython_execlines` are
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executed. If not specified in conf.py, then the default value of 'agg' is
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used. To use the yap_ipython directive without matplotlib as a dependency, set
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the value to `None`. It may end up that matplotlib is still imported
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if the user specifies so in `ipython_execlines` or makes use of the
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@savefig pseudo decorator.
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ipython_execlines:
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A list of strings to be exec'd in the embedded Sphinx shell. Typical
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usage is to make certain packages always available. Set this to an empty
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list if you wish to have no imports always available. If specified in
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conf.py as `None`, then it has the effect of making no imports available.
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If omitted from conf.py altogether, then the default value of
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['import numpy as np', 'import matplotlib.pyplot as plt'] is used.
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ipython_holdcount
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When the @suppress pseudo-decorator is used, the execution count can be
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incremented or not. The default behavior is to hold the execution count,
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corresponding to a value of `True`. Set this to `False` to increment
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the execution count after each suppressed command.
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As an example, to use the yap_ipython directive when `matplotlib` is not available,
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one sets the backend to `None`::
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ipython_mplbackend = None
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An example usage of the directive is:
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.. code-block:: rst
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.. ipython::
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In [1]: x = 1
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In [2]: y = x**2
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In [3]: print(y)
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See http://matplotlib.org/sampledoc/ipython_directive.html for additional
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documentation.
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Pseudo-Decorators
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=================
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Note: Only one decorator is supported per input. If more than one decorator
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is specified, then only the last one is used.
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In addition to the Pseudo-Decorators/options described at the above link,
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several enhancements have been made. The directive will emit a message to the
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console at build-time if code-execution resulted in an exception or warning.
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You can suppress these on a per-block basis by specifying the :okexcept:
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or :okwarning: options:
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.. code-block:: rst
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.. ipython::
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:okexcept:
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:okwarning:
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In [1]: 1/0
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In [2]: # raise warning.
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To Do
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-----
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- Turn the ad-hoc test() function into a real test suite.
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- Break up ipython-specific functionality from matplotlib stuff into better
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separated code.
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Authors
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-------
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- John D Hunter: orignal author.
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- Fernando Perez: refactoring, documentation, cleanups, port to 0.11.
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- VáclavŠmilauer <eudoxos-AT-arcig.cz>: Prompt generalizations.
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- Skipper Seabold, refactoring, cleanups, pure python addition
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"""
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#-----------------------------------------------------------------------------
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# Imports
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#-----------------------------------------------------------------------------
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# Stdlib
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import atexit
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import errno
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import os
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import re
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import sys
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import tempfile
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import ast
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import warnings
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import shutil
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from io import StringIO
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# Third-party
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from docutils.parsers.rst import directives
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from docutils.parsers.rst import Directive
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# Our own
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from traitlets.config import Config
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from yap_ipython import InteractiveShell
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from yap_ipython.core.profiledir import ProfileDir
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#-----------------------------------------------------------------------------
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# Globals
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#-----------------------------------------------------------------------------
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# for tokenizing blocks
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COMMENT, INPUT, OUTPUT = range(3)
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#-----------------------------------------------------------------------------
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# Functions and class declarations
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#-----------------------------------------------------------------------------
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def block_parser(part, rgxin, rgxout, fmtin, fmtout):
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"""
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part is a string of ipython text, comprised of at most one
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input, one output, comments, and blank lines. The block parser
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parses the text into a list of::
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blocks = [ (TOKEN0, data0), (TOKEN1, data1), ...]
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where TOKEN is one of [COMMENT | INPUT | OUTPUT ] and
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data is, depending on the type of token::
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COMMENT : the comment string
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INPUT: the (DECORATOR, INPUT_LINE, REST) where
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DECORATOR: the input decorator (or None)
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INPUT_LINE: the input as string (possibly multi-line)
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REST : any stdout generated by the input line (not OUTPUT)
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OUTPUT: the output string, possibly multi-line
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"""
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block = []
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lines = part.split('\n')
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N = len(lines)
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i = 0
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decorator = None
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while 1:
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if i==N:
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# nothing left to parse -- the last line
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break
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line = lines[i]
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i += 1
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line_stripped = line.strip()
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if line_stripped.startswith('#'):
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block.append((COMMENT, line))
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continue
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if line_stripped.startswith('@'):
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# Here is where we assume there is, at most, one decorator.
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# Might need to rethink this.
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decorator = line_stripped
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continue
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# does this look like an input line?
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matchin = rgxin.match(line)
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if matchin:
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lineno, inputline = int(matchin.group(1)), matchin.group(2)
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# the ....: continuation string
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continuation = ' %s:'%''.join(['.']*(len(str(lineno))+2))
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Nc = len(continuation)
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# input lines can continue on for more than one line, if
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# we have a '\' line continuation char or a function call
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# echo line 'print'. The input line can only be
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# terminated by the end of the block or an output line, so
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# we parse out the rest of the input line if it is
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# multiline as well as any echo text
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rest = []
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while i<N:
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# look ahead; if the next line is blank, or a comment, or
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# an output line, we're done
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nextline = lines[i]
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matchout = rgxout.match(nextline)
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#print "nextline=%s, continuation=%s, starts=%s"%(nextline, continuation, nextline.startswith(continuation))
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if matchout or nextline.startswith('#'):
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break
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elif nextline.startswith(continuation):
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# The default ipython_rgx* treat the space following the colon as optional.
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# However, If the space is there we must consume it or code
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# employing the cython_magic extension will fail to execute.
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#
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# This works with the default ipython_rgx* patterns,
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# If you modify them, YMMV.
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nextline = nextline[Nc:]
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if nextline and nextline[0] == ' ':
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nextline = nextline[1:]
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inputline += '\n' + nextline
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else:
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rest.append(nextline)
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i+= 1
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block.append((INPUT, (decorator, inputline, '\n'.join(rest))))
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continue
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# if it looks like an output line grab all the text to the end
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# of the block
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matchout = rgxout.match(line)
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if matchout:
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lineno, output = int(matchout.group(1)), matchout.group(2)
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if i<N-1:
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output = '\n'.join([output] + lines[i:])
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block.append((OUTPUT, output))
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break
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return block
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class EmbeddedSphinxShell(object):
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"""An embedded yap_ipython instance to run inside Sphinx"""
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def __init__(self, exec_lines=None):
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self.cout = StringIO()
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if exec_lines is None:
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exec_lines = []
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# Create config object for yap_ipython
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config = Config()
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config.HistoryManager.hist_file = ':memory:'
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config.InteractiveShell.autocall = False
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config.InteractiveShell.autoindent = False
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config.InteractiveShell.colors = 'NoColor'
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# create a profile so instance history isn't saved
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tmp_profile_dir = tempfile.mkdtemp(prefix='profile_')
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profname = 'auto_profile_sphinx_build'
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pdir = os.path.join(tmp_profile_dir,profname)
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profile = ProfileDir.create_profile_dir(pdir)
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# Create and initialize global ipython, but don't start its mainloop.
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# This will persist across different EmbeddedSphinxShell instances.
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IP = InteractiveShell.instance(config=config, profile_dir=profile)
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atexit.register(self.cleanup)
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# Store a few parts of yap_ipython we'll need.
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self.IP = IP
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self.user_ns = self.IP.user_ns
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self.user_global_ns = self.IP.user_global_ns
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self.input = ''
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self.output = ''
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self.tmp_profile_dir = tmp_profile_dir
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self.is_verbatim = False
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self.is_doctest = False
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self.is_suppress = False
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# Optionally, provide more detailed information to shell.
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# this is assigned by the SetUp method of IPythonDirective
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# to point at itself.
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#
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# So, you can access handy things at self.directive.state
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self.directive = None
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# on the first call to the savefig decorator, we'll import
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# pyplot as plt so we can make a call to the plt.gcf().savefig
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self._pyplot_imported = False
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# Prepopulate the namespace.
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for line in exec_lines:
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self.process_input_line(line, store_history=False)
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def cleanup(self):
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shutil.rmtree(self.tmp_profile_dir, ignore_errors=True)
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def clear_cout(self):
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self.cout.seek(0)
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self.cout.truncate(0)
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def process_input_line(self, line, store_history=True):
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"""process the input, capturing stdout"""
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stdout = sys.stdout
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splitter = self.IP.input_splitter
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try:
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sys.stdout = self.cout
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splitter.push(line)
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more = splitter.push_accepts_more()
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if not more:
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source_raw = splitter.raw_reset()
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self.IP.run_cell(source_raw, store_history=store_history)
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finally:
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sys.stdout = stdout
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def process_image(self, decorator):
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"""
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# build out an image directive like
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# .. image:: somefile.png
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# :width 4in
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#
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# from an input like
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# savefig somefile.png width=4in
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"""
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savefig_dir = self.savefig_dir
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source_dir = self.source_dir
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saveargs = decorator.split(' ')
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filename = saveargs[1]
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# insert relative path to image file in source (as absolute path for Sphinx)
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outfile = '/' + os.path.relpath(os.path.join(savefig_dir,filename),
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source_dir)
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imagerows = ['.. image:: %s'%outfile]
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for kwarg in saveargs[2:]:
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arg, val = kwarg.split('=')
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arg = arg.strip()
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val = val.strip()
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imagerows.append(' :%s: %s'%(arg, val))
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image_file = os.path.basename(outfile) # only return file name
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image_directive = '\n'.join(imagerows)
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return image_file, image_directive
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# Callbacks for each type of token
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def process_input(self, data, input_prompt, lineno):
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"""
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Process data block for INPUT token.
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"""
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|
|
decorator, input, rest = data
|
||
|
|
image_file = None
|
||
|
|
image_directive = None
|
||
|
|
|
||
|
|
is_verbatim = decorator=='@verbatim' or self.is_verbatim
|
||
|
|
is_doctest = (decorator is not None and \
|
||
|
|
decorator.startswith('@doctest')) or self.is_doctest
|
||
|
|
is_suppress = decorator=='@suppress' or self.is_suppress
|
||
|
|
is_okexcept = decorator=='@okexcept' or self.is_okexcept
|
||
|
|
is_okwarning = decorator=='@okwarning' or self.is_okwarning
|
||
|
|
is_savefig = decorator is not None and \
|
||
|
|
decorator.startswith('@savefig')
|
||
|
|
|
||
|
|
input_lines = input.split('\n')
|
||
|
|
if len(input_lines) > 1:
|
||
|
|
if input_lines[-1] != "":
|
||
|
|
input_lines.append('') # make sure there's a blank line
|
||
|
|
# so splitter buffer gets reset
|
||
|
|
|
||
|
|
continuation = ' %s:'%''.join(['.']*(len(str(lineno))+2))
|
||
|
|
|
||
|
|
if is_savefig:
|
||
|
|
image_file, image_directive = self.process_image(decorator)
|
||
|
|
|
||
|
|
ret = []
|
||
|
|
is_semicolon = False
|
||
|
|
|
||
|
|
# Hold the execution count, if requested to do so.
|
||
|
|
if is_suppress and self.hold_count:
|
||
|
|
store_history = False
|
||
|
|
else:
|
||
|
|
store_history = True
|
||
|
|
|
||
|
|
# Note: catch_warnings is not thread safe
|
||
|
|
with warnings.catch_warnings(record=True) as ws:
|
||
|
|
for i, line in enumerate(input_lines):
|
||
|
|
if line.endswith(';'):
|
||
|
|
is_semicolon = True
|
||
|
|
|
||
|
|
if i == 0:
|
||
|
|
# process the first input line
|
||
|
|
if is_verbatim:
|
||
|
|
self.process_input_line('')
|
||
|
|
self.IP.execution_count += 1 # increment it anyway
|
||
|
|
else:
|
||
|
|
# only submit the line in non-verbatim mode
|
||
|
|
self.process_input_line(line, store_history=store_history)
|
||
|
|
formatted_line = '%s %s'%(input_prompt, line)
|
||
|
|
else:
|
||
|
|
# process a continuation line
|
||
|
|
if not is_verbatim:
|
||
|
|
self.process_input_line(line, store_history=store_history)
|
||
|
|
|
||
|
|
formatted_line = '%s %s'%(continuation, line)
|
||
|
|
|
||
|
|
if not is_suppress:
|
||
|
|
ret.append(formatted_line)
|
||
|
|
|
||
|
|
if not is_suppress and len(rest.strip()) and is_verbatim:
|
||
|
|
# The "rest" is the standard output of the input. This needs to be
|
||
|
|
# added when in verbatim mode. If there is no "rest", then we don't
|
||
|
|
# add it, as the new line will be added by the processed output.
|
||
|
|
ret.append(rest)
|
||
|
|
|
||
|
|
# Fetch the processed output. (This is not the submitted output.)
|
||
|
|
self.cout.seek(0)
|
||
|
|
processed_output = self.cout.read()
|
||
|
|
if not is_suppress and not is_semicolon:
|
||
|
|
#
|
||
|
|
# In IPythonDirective.run, the elements of `ret` are eventually
|
||
|
|
# combined such that '' entries correspond to newlines. So if
|
||
|
|
# `processed_output` is equal to '', then the adding it to `ret`
|
||
|
|
# ensures that there is a blank line between consecutive inputs
|
||
|
|
# that have no outputs, as in:
|
||
|
|
#
|
||
|
|
# In [1]: x = 4
|
||
|
|
#
|
||
|
|
# In [2]: x = 5
|
||
|
|
#
|
||
|
|
# When there is processed output, it has a '\n' at the tail end. So
|
||
|
|
# adding the output to `ret` will provide the necessary spacing
|
||
|
|
# between consecutive input/output blocks, as in:
|
||
|
|
#
|
||
|
|
# In [1]: x
|
||
|
|
# Out[1]: 5
|
||
|
|
#
|
||
|
|
# In [2]: x
|
||
|
|
# Out[2]: 5
|
||
|
|
#
|
||
|
|
# When there is stdout from the input, it also has a '\n' at the
|
||
|
|
# tail end, and so this ensures proper spacing as well. E.g.:
|
||
|
|
#
|
||
|
|
# In [1]: print x
|
||
|
|
# 5
|
||
|
|
#
|
||
|
|
# In [2]: x = 5
|
||
|
|
#
|
||
|
|
# When in verbatim mode, `processed_output` is empty (because
|
||
|
|
# nothing was passed to IP. Sometimes the submitted code block has
|
||
|
|
# an Out[] portion and sometimes it does not. When it does not, we
|
||
|
|
# need to ensure proper spacing, so we have to add '' to `ret`.
|
||
|
|
# However, if there is an Out[] in the submitted code, then we do
|
||
|
|
# not want to add a newline as `process_output` has stuff to add.
|
||
|
|
# The difficulty is that `process_input` doesn't know if
|
||
|
|
# `process_output` will be called---so it doesn't know if there is
|
||
|
|
# Out[] in the code block. The requires that we include a hack in
|
||
|
|
# `process_block`. See the comments there.
|
||
|
|
#
|
||
|
|
ret.append(processed_output)
|
||
|
|
elif is_semicolon:
|
||
|
|
# Make sure there is a newline after the semicolon.
|
||
|
|
ret.append('')
|
||
|
|
|
||
|
|
# context information
|
||
|
|
filename = "Unknown"
|
||
|
|
lineno = 0
|
||
|
|
if self.directive.state:
|
||
|
|
filename = self.directive.state.document.current_source
|
||
|
|
lineno = self.directive.state.document.current_line
|
||
|
|
|
||
|
|
# output any exceptions raised during execution to stdout
|
||
|
|
# unless :okexcept: has been specified.
|
||
|
|
if not is_okexcept and "Traceback" in processed_output:
|
||
|
|
s = "\nException in %s at block ending on line %s\n" % (filename, lineno)
|
||
|
|
s += "Specify :okexcept: as an option in the ipython:: block to suppress this message\n"
|
||
|
|
sys.stdout.write('\n\n>>>' + ('-' * 73))
|
||
|
|
sys.stdout.write(s)
|
||
|
|
sys.stdout.write(processed_output)
|
||
|
|
sys.stdout.write('<<<' + ('-' * 73) + '\n\n')
|
||
|
|
|
||
|
|
# output any warning raised during execution to stdout
|
||
|
|
# unless :okwarning: has been specified.
|
||
|
|
if not is_okwarning:
|
||
|
|
for w in ws:
|
||
|
|
s = "\nWarning in %s at block ending on line %s\n" % (filename, lineno)
|
||
|
|
s += "Specify :okwarning: as an option in the ipython:: block to suppress this message\n"
|
||
|
|
sys.stdout.write('\n\n>>>' + ('-' * 73))
|
||
|
|
sys.stdout.write(s)
|
||
|
|
sys.stdout.write(('-' * 76) + '\n')
|
||
|
|
s=warnings.formatwarning(w.message, w.category,
|
||
|
|
w.filename, w.lineno, w.line)
|
||
|
|
sys.stdout.write(s)
|
||
|
|
sys.stdout.write('<<<' + ('-' * 73) + '\n')
|
||
|
|
|
||
|
|
self.cout.truncate(0)
|
||
|
|
|
||
|
|
return (ret, input_lines, processed_output,
|
||
|
|
is_doctest, decorator, image_file, image_directive)
|
||
|
|
|
||
|
|
|
||
|
|
def process_output(self, data, output_prompt, input_lines, output,
|
||
|
|
is_doctest, decorator, image_file):
|
||
|
|
"""
|
||
|
|
Process data block for OUTPUT token.
|
||
|
|
|
||
|
|
"""
|
||
|
|
# Recall: `data` is the submitted output, and `output` is the processed
|
||
|
|
# output from `input_lines`.
|
||
|
|
|
||
|
|
TAB = ' ' * 4
|
||
|
|
|
||
|
|
if is_doctest and output is not None:
|
||
|
|
|
||
|
|
found = output # This is the processed output
|
||
|
|
found = found.strip()
|
||
|
|
submitted = data.strip()
|
||
|
|
|
||
|
|
if self.directive is None:
|
||
|
|
source = 'Unavailable'
|
||
|
|
content = 'Unavailable'
|
||
|
|
else:
|
||
|
|
source = self.directive.state.document.current_source
|
||
|
|
content = self.directive.content
|
||
|
|
# Add tabs and join into a single string.
|
||
|
|
content = '\n'.join([TAB + line for line in content])
|
||
|
|
|
||
|
|
# Make sure the output contains the output prompt.
|
||
|
|
ind = found.find(output_prompt)
|
||
|
|
if ind < 0:
|
||
|
|
e = ('output does not contain output prompt\n\n'
|
||
|
|
'Document source: {0}\n\n'
|
||
|
|
'Raw content: \n{1}\n\n'
|
||
|
|
'Input line(s):\n{TAB}{2}\n\n'
|
||
|
|
'Output line(s):\n{TAB}{3}\n\n')
|
||
|
|
e = e.format(source, content, '\n'.join(input_lines),
|
||
|
|
repr(found), TAB=TAB)
|
||
|
|
raise RuntimeError(e)
|
||
|
|
found = found[len(output_prompt):].strip()
|
||
|
|
|
||
|
|
# Handle the actual doctest comparison.
|
||
|
|
if decorator.strip() == '@doctest':
|
||
|
|
# Standard doctest
|
||
|
|
if found != submitted:
|
||
|
|
e = ('doctest failure\n\n'
|
||
|
|
'Document source: {0}\n\n'
|
||
|
|
'Raw content: \n{1}\n\n'
|
||
|
|
'On input line(s):\n{TAB}{2}\n\n'
|
||
|
|
'we found output:\n{TAB}{3}\n\n'
|
||
|
|
'instead of the expected:\n{TAB}{4}\n\n')
|
||
|
|
e = e.format(source, content, '\n'.join(input_lines),
|
||
|
|
repr(found), repr(submitted), TAB=TAB)
|
||
|
|
raise RuntimeError(e)
|
||
|
|
else:
|
||
|
|
self.custom_doctest(decorator, input_lines, found, submitted)
|
||
|
|
|
||
|
|
# When in verbatim mode, this holds additional submitted output
|
||
|
|
# to be written in the final Sphinx output.
|
||
|
|
# https://github.com/ipython/ipython/issues/5776
|
||
|
|
out_data = []
|
||
|
|
|
||
|
|
is_verbatim = decorator=='@verbatim' or self.is_verbatim
|
||
|
|
if is_verbatim and data.strip():
|
||
|
|
# Note that `ret` in `process_block` has '' as its last element if
|
||
|
|
# the code block was in verbatim mode. So if there is no submitted
|
||
|
|
# output, then we will have proper spacing only if we do not add
|
||
|
|
# an additional '' to `out_data`. This is why we condition on
|
||
|
|
# `and data.strip()`.
|
||
|
|
|
||
|
|
# The submitted output has no output prompt. If we want the
|
||
|
|
# prompt and the code to appear, we need to join them now
|
||
|
|
# instead of adding them separately---as this would create an
|
||
|
|
# undesired newline. How we do this ultimately depends on the
|
||
|
|
# format of the output regex. I'll do what works for the default
|
||
|
|
# prompt for now, and we might have to adjust if it doesn't work
|
||
|
|
# in other cases. Finally, the submitted output does not have
|
||
|
|
# a trailing newline, so we must add it manually.
|
||
|
|
out_data.append("{0} {1}\n".format(output_prompt, data))
|
||
|
|
|
||
|
|
return out_data
|
||
|
|
|
||
|
|
def process_comment(self, data):
|
||
|
|
"""Process data fPblock for COMMENT token."""
|
||
|
|
if not self.is_suppress:
|
||
|
|
return [data]
|
||
|
|
|
||
|
|
def save_image(self, image_file):
|
||
|
|
"""
|
||
|
|
Saves the image file to disk.
|
||
|
|
"""
|
||
|
|
self.ensure_pyplot()
|
||
|
|
command = 'plt.gcf().savefig("%s")'%image_file
|
||
|
|
#print 'SAVEFIG', command # dbg
|
||
|
|
self.process_input_line('bookmark ipy_thisdir', store_history=False)
|
||
|
|
self.process_input_line('cd -b ipy_savedir', store_history=False)
|
||
|
|
self.process_input_line(command, store_history=False)
|
||
|
|
self.process_input_line('cd -b ipy_thisdir', store_history=False)
|
||
|
|
self.process_input_line('bookmark -d ipy_thisdir', store_history=False)
|
||
|
|
self.clear_cout()
|
||
|
|
|
||
|
|
def process_block(self, block):
|
||
|
|
"""
|
||
|
|
process block from the block_parser and return a list of processed lines
|
||
|
|
"""
|
||
|
|
ret = []
|
||
|
|
output = None
|
||
|
|
input_lines = None
|
||
|
|
lineno = self.IP.execution_count
|
||
|
|
|
||
|
|
input_prompt = self.promptin % lineno
|
||
|
|
output_prompt = self.promptout % lineno
|
||
|
|
image_file = None
|
||
|
|
image_directive = None
|
||
|
|
|
||
|
|
found_input = False
|
||
|
|
for token, data in block:
|
||
|
|
if token == COMMENT:
|
||
|
|
out_data = self.process_comment(data)
|
||
|
|
elif token == INPUT:
|
||
|
|
found_input = True
|
||
|
|
(out_data, input_lines, output, is_doctest,
|
||
|
|
decorator, image_file, image_directive) = \
|
||
|
|
self.process_input(data, input_prompt, lineno)
|
||
|
|
elif token == OUTPUT:
|
||
|
|
if not found_input:
|
||
|
|
|
||
|
|
TAB = ' ' * 4
|
||
|
|
linenumber = 0
|
||
|
|
source = 'Unavailable'
|
||
|
|
content = 'Unavailable'
|
||
|
|
if self.directive:
|
||
|
|
linenumber = self.directive.state.document.current_line
|
||
|
|
source = self.directive.state.document.current_source
|
||
|
|
content = self.directive.content
|
||
|
|
# Add tabs and join into a single string.
|
||
|
|
content = '\n'.join([TAB + line for line in content])
|
||
|
|
|
||
|
|
e = ('\n\nInvalid block: Block contains an output prompt '
|
||
|
|
'without an input prompt.\n\n'
|
||
|
|
'Document source: {0}\n\n'
|
||
|
|
'Content begins at line {1}: \n\n{2}\n\n'
|
||
|
|
'Problematic block within content: \n\n{TAB}{3}\n\n')
|
||
|
|
e = e.format(source, linenumber, content, block, TAB=TAB)
|
||
|
|
|
||
|
|
# Write, rather than include in exception, since Sphinx
|
||
|
|
# will truncate tracebacks.
|
||
|
|
sys.stdout.write(e)
|
||
|
|
raise RuntimeError('An invalid block was detected.')
|
||
|
|
|
||
|
|
out_data = \
|
||
|
|
self.process_output(data, output_prompt, input_lines,
|
||
|
|
output, is_doctest, decorator,
|
||
|
|
image_file)
|
||
|
|
if out_data:
|
||
|
|
# Then there was user submitted output in verbatim mode.
|
||
|
|
# We need to remove the last element of `ret` that was
|
||
|
|
# added in `process_input`, as it is '' and would introduce
|
||
|
|
# an undesirable newline.
|
||
|
|
assert(ret[-1] == '')
|
||
|
|
del ret[-1]
|
||
|
|
|
||
|
|
if out_data:
|
||
|
|
ret.extend(out_data)
|
||
|
|
|
||
|
|
# save the image files
|
||
|
|
if image_file is not None:
|
||
|
|
self.save_image(image_file)
|
||
|
|
|
||
|
|
return ret, image_directive
|
||
|
|
|
||
|
|
def ensure_pyplot(self):
|
||
|
|
"""
|
||
|
|
Ensures that pyplot has been imported into the embedded yap_ipython shell.
|
||
|
|
|
||
|
|
Also, makes sure to set the backend appropriately if not set already.
|
||
|
|
|
||
|
|
"""
|
||
|
|
# We are here if the @figure pseudo decorator was used. Thus, it's
|
||
|
|
# possible that we could be here even if python_mplbackend were set to
|
||
|
|
# `None`. That's also strange and perhaps worthy of raising an
|
||
|
|
# exception, but for now, we just set the backend to 'agg'.
|
||
|
|
|
||
|
|
if not self._pyplot_imported:
|
||
|
|
if 'matplotlib.backends' not in sys.modules:
|
||
|
|
# Then ipython_matplotlib was set to None but there was a
|
||
|
|
# call to the @figure decorator (and ipython_execlines did
|
||
|
|
# not set a backend).
|
||
|
|
#raise Exception("No backend was set, but @figure was used!")
|
||
|
|
import matplotlib
|
||
|
|
matplotlib.use('agg')
|
||
|
|
|
||
|
|
# Always import pyplot into embedded shell.
|
||
|
|
self.process_input_line('import matplotlib.pyplot as plt',
|
||
|
|
store_history=False)
|
||
|
|
self._pyplot_imported = True
|
||
|
|
|
||
|
|
def process_pure_python(self, content):
|
||
|
|
"""
|
||
|
|
content is a list of strings. it is unedited directive content
|
||
|
|
|
||
|
|
This runs it line by line in the InteractiveShell, prepends
|
||
|
|
prompts as needed capturing stderr and stdout, then returns
|
||
|
|
the content as a list as if it were ipython code
|
||
|
|
"""
|
||
|
|
output = []
|
||
|
|
savefig = False # keep up with this to clear figure
|
||
|
|
multiline = False # to handle line continuation
|
||
|
|
multiline_start = None
|
||
|
|
fmtin = self.promptin
|
||
|
|
|
||
|
|
ct = 0
|
||
|
|
|
||
|
|
for lineno, line in enumerate(content):
|
||
|
|
|
||
|
|
line_stripped = line.strip()
|
||
|
|
if not len(line):
|
||
|
|
output.append(line)
|
||
|
|
continue
|
||
|
|
|
||
|
|
# handle decorators
|
||
|
|
if line_stripped.startswith('@'):
|
||
|
|
output.extend([line])
|
||
|
|
if 'savefig' in line:
|
||
|
|
savefig = True # and need to clear figure
|
||
|
|
continue
|
||
|
|
|
||
|
|
# handle comments
|
||
|
|
if line_stripped.startswith('#'):
|
||
|
|
output.extend([line])
|
||
|
|
continue
|
||
|
|
|
||
|
|
# deal with lines checking for multiline
|
||
|
|
continuation = u' %s:'% ''.join(['.']*(len(str(ct))+2))
|
||
|
|
if not multiline:
|
||
|
|
modified = u"%s %s" % (fmtin % ct, line_stripped)
|
||
|
|
output.append(modified)
|
||
|
|
ct += 1
|
||
|
|
try:
|
||
|
|
ast.parse(line_stripped)
|
||
|
|
output.append(u'')
|
||
|
|
except Exception: # on a multiline
|
||
|
|
multiline = True
|
||
|
|
multiline_start = lineno
|
||
|
|
else: # still on a multiline
|
||
|
|
modified = u'%s %s' % (continuation, line)
|
||
|
|
output.append(modified)
|
||
|
|
|
||
|
|
# if the next line is indented, it should be part of multiline
|
||
|
|
if len(content) > lineno + 1:
|
||
|
|
nextline = content[lineno + 1]
|
||
|
|
if len(nextline) - len(nextline.lstrip()) > 3:
|
||
|
|
continue
|
||
|
|
try:
|
||
|
|
mod = ast.parse(
|
||
|
|
'\n'.join(content[multiline_start:lineno+1]))
|
||
|
|
if isinstance(mod.body[0], ast.FunctionDef):
|
||
|
|
# check to see if we have the whole function
|
||
|
|
for element in mod.body[0].body:
|
||
|
|
if isinstance(element, ast.Return):
|
||
|
|
multiline = False
|
||
|
|
else:
|
||
|
|
output.append(u'')
|
||
|
|
multiline = False
|
||
|
|
except Exception:
|
||
|
|
pass
|
||
|
|
|
||
|
|
if savefig: # clear figure if plotted
|
||
|
|
self.ensure_pyplot()
|
||
|
|
self.process_input_line('plt.clf()', store_history=False)
|
||
|
|
self.clear_cout()
|
||
|
|
savefig = False
|
||
|
|
|
||
|
|
return output
|
||
|
|
|
||
|
|
def custom_doctest(self, decorator, input_lines, found, submitted):
|
||
|
|
"""
|
||
|
|
Perform a specialized doctest.
|
||
|
|
|
||
|
|
"""
|
||
|
|
from .custom_doctests import doctests
|
||
|
|
|
||
|
|
args = decorator.split()
|
||
|
|
doctest_type = args[1]
|
||
|
|
if doctest_type in doctests:
|
||
|
|
doctests[doctest_type](self, args, input_lines, found, submitted)
|
||
|
|
else:
|
||
|
|
e = "Invalid option to @doctest: {0}".format(doctest_type)
|
||
|
|
raise Exception(e)
|
||
|
|
|
||
|
|
|
||
|
|
class IPythonDirective(Directive):
|
||
|
|
|
||
|
|
has_content = True
|
||
|
|
required_arguments = 0
|
||
|
|
optional_arguments = 4 # python, suppress, verbatim, doctest
|
||
|
|
final_argumuent_whitespace = True
|
||
|
|
option_spec = { 'python': directives.unchanged,
|
||
|
|
'suppress' : directives.flag,
|
||
|
|
'verbatim' : directives.flag,
|
||
|
|
'doctest' : directives.flag,
|
||
|
|
'okexcept': directives.flag,
|
||
|
|
'okwarning': directives.flag
|
||
|
|
}
|
||
|
|
|
||
|
|
shell = None
|
||
|
|
|
||
|
|
seen_docs = set()
|
||
|
|
|
||
|
|
def get_config_options(self):
|
||
|
|
# contains sphinx configuration variables
|
||
|
|
config = self.state.document.settings.env.config
|
||
|
|
|
||
|
|
# get config variables to set figure output directory
|
||
|
|
savefig_dir = config.ipython_savefig_dir
|
||
|
|
source_dir = self.state.document.settings.env.srcdir
|
||
|
|
savefig_dir = os.path.join(source_dir, savefig_dir)
|
||
|
|
|
||
|
|
# get regex and prompt stuff
|
||
|
|
rgxin = config.ipython_rgxin
|
||
|
|
rgxout = config.ipython_rgxout
|
||
|
|
promptin = config.ipython_promptin
|
||
|
|
promptout = config.ipython_promptout
|
||
|
|
mplbackend = config.ipython_mplbackend
|
||
|
|
exec_lines = config.ipython_execlines
|
||
|
|
hold_count = config.ipython_holdcount
|
||
|
|
|
||
|
|
return (savefig_dir, source_dir, rgxin, rgxout,
|
||
|
|
promptin, promptout, mplbackend, exec_lines, hold_count)
|
||
|
|
|
||
|
|
def setup(self):
|
||
|
|
# Get configuration values.
|
||
|
|
(savefig_dir, source_dir, rgxin, rgxout, promptin, promptout,
|
||
|
|
mplbackend, exec_lines, hold_count) = self.get_config_options()
|
||
|
|
|
||
|
|
try:
|
||
|
|
os.makedirs(savefig_dir)
|
||
|
|
except OSError as e:
|
||
|
|
if e.errno != errno.EEXIST:
|
||
|
|
raise
|
||
|
|
|
||
|
|
if self.shell is None:
|
||
|
|
# We will be here many times. However, when the
|
||
|
|
# EmbeddedSphinxShell is created, its interactive shell member
|
||
|
|
# is the same for each instance.
|
||
|
|
|
||
|
|
if mplbackend and 'matplotlib.backends' not in sys.modules:
|
||
|
|
import matplotlib
|
||
|
|
matplotlib.use(mplbackend)
|
||
|
|
|
||
|
|
# Must be called after (potentially) importing matplotlib and
|
||
|
|
# setting its backend since exec_lines might import pylab.
|
||
|
|
self.shell = EmbeddedSphinxShell(exec_lines)
|
||
|
|
|
||
|
|
# Store yap_ipython directive to enable better error messages
|
||
|
|
self.shell.directive = self
|
||
|
|
|
||
|
|
# reset the execution count if we haven't processed this doc
|
||
|
|
#NOTE: this may be borked if there are multiple seen_doc tmp files
|
||
|
|
#check time stamp?
|
||
|
|
if not self.state.document.current_source in self.seen_docs:
|
||
|
|
self.shell.IP.history_manager.reset()
|
||
|
|
self.shell.IP.execution_count = 1
|
||
|
|
self.seen_docs.add(self.state.document.current_source)
|
||
|
|
|
||
|
|
# and attach to shell so we don't have to pass them around
|
||
|
|
self.shell.rgxin = rgxin
|
||
|
|
self.shell.rgxout = rgxout
|
||
|
|
self.shell.promptin = promptin
|
||
|
|
self.shell.promptout = promptout
|
||
|
|
self.shell.savefig_dir = savefig_dir
|
||
|
|
self.shell.source_dir = source_dir
|
||
|
|
self.shell.hold_count = hold_count
|
||
|
|
|
||
|
|
# setup bookmark for saving figures directory
|
||
|
|
self.shell.process_input_line('bookmark ipy_savedir %s'%savefig_dir,
|
||
|
|
store_history=False)
|
||
|
|
self.shell.clear_cout()
|
||
|
|
|
||
|
|
return rgxin, rgxout, promptin, promptout
|
||
|
|
|
||
|
|
def teardown(self):
|
||
|
|
# delete last bookmark
|
||
|
|
self.shell.process_input_line('bookmark -d ipy_savedir',
|
||
|
|
store_history=False)
|
||
|
|
self.shell.clear_cout()
|
||
|
|
|
||
|
|
def run(self):
|
||
|
|
debug = False
|
||
|
|
|
||
|
|
#TODO, any reason block_parser can't be a method of embeddable shell
|
||
|
|
# then we wouldn't have to carry these around
|
||
|
|
rgxin, rgxout, promptin, promptout = self.setup()
|
||
|
|
|
||
|
|
options = self.options
|
||
|
|
self.shell.is_suppress = 'suppress' in options
|
||
|
|
self.shell.is_doctest = 'doctest' in options
|
||
|
|
self.shell.is_verbatim = 'verbatim' in options
|
||
|
|
self.shell.is_okexcept = 'okexcept' in options
|
||
|
|
self.shell.is_okwarning = 'okwarning' in options
|
||
|
|
|
||
|
|
# handle pure python code
|
||
|
|
if 'python' in self.arguments:
|
||
|
|
content = self.content
|
||
|
|
self.content = self.shell.process_pure_python(content)
|
||
|
|
|
||
|
|
# parts consists of all text within the ipython-block.
|
||
|
|
# Each part is an input/output block.
|
||
|
|
parts = '\n'.join(self.content).split('\n\n')
|
||
|
|
|
||
|
|
lines = ['.. code-block:: ipython', '']
|
||
|
|
figures = []
|
||
|
|
|
||
|
|
for part in parts:
|
||
|
|
block = block_parser(part, rgxin, rgxout, promptin, promptout)
|
||
|
|
if len(block):
|
||
|
|
rows, figure = self.shell.process_block(block)
|
||
|
|
for row in rows:
|
||
|
|
lines.extend([' {0}'.format(line)
|
||
|
|
for line in row.split('\n')])
|
||
|
|
|
||
|
|
if figure is not None:
|
||
|
|
figures.append(figure)
|
||
|
|
|
||
|
|
for figure in figures:
|
||
|
|
lines.append('')
|
||
|
|
lines.extend(figure.split('\n'))
|
||
|
|
lines.append('')
|
||
|
|
|
||
|
|
if len(lines) > 2:
|
||
|
|
if debug:
|
||
|
|
print('\n'.join(lines))
|
||
|
|
else:
|
||
|
|
# This has to do with input, not output. But if we comment
|
||
|
|
# these lines out, then no yap_ipython code will appear in the
|
||
|
|
# final output.
|
||
|
|
self.state_machine.insert_input(
|
||
|
|
lines, self.state_machine.input_lines.source(0))
|
||
|
|
|
||
|
|
# cleanup
|
||
|
|
self.teardown()
|
||
|
|
|
||
|
|
return []
|
||
|
|
|
||
|
|
# Enable as a proper Sphinx directive
|
||
|
|
def setup(app):
|
||
|
|
setup.app = app
|
||
|
|
|
||
|
|
app.add_directive('ipython', IPythonDirective)
|
||
|
|
app.add_config_value('ipython_savefig_dir', 'savefig', 'env')
|
||
|
|
app.add_config_value('ipython_rgxin',
|
||
|
|
re.compile('In \[(\d+)\]:\s?(.*)\s*'), 'env')
|
||
|
|
app.add_config_value('ipython_rgxout',
|
||
|
|
re.compile('Out\[(\d+)\]:\s?(.*)\s*'), 'env')
|
||
|
|
app.add_config_value('ipython_promptin', 'In [%d]:', 'env')
|
||
|
|
app.add_config_value('ipython_promptout', 'Out[%d]:', 'env')
|
||
|
|
|
||
|
|
# We could just let matplotlib pick whatever is specified as the default
|
||
|
|
# backend in the matplotlibrc file, but this would cause issues if the
|
||
|
|
# backend didn't work in headless environments. For this reason, 'agg'
|
||
|
|
# is a good default backend choice.
|
||
|
|
app.add_config_value('ipython_mplbackend', 'agg', 'env')
|
||
|
|
|
||
|
|
# If the user sets this config value to `None`, then EmbeddedSphinxShell's
|
||
|
|
# __init__ method will treat it as [].
|
||
|
|
execlines = ['import numpy as np', 'import matplotlib.pyplot as plt']
|
||
|
|
app.add_config_value('ipython_execlines', execlines, 'env')
|
||
|
|
|
||
|
|
app.add_config_value('ipython_holdcount', True, 'env')
|
||
|
|
|
||
|
|
metadata = {'parallel_read_safe': True, 'parallel_write_safe': True}
|
||
|
|
return metadata
|
||
|
|
|
||
|
|
# Simple smoke test, needs to be converted to a proper automatic test.
|
||
|
|
def test():
|
||
|
|
|
||
|
|
examples = [
|
||
|
|
r"""
|
||
|
|
In [9]: pwd
|
||
|
|
Out[9]: '/home/jdhunter/py4science/book'
|
||
|
|
|
||
|
|
In [10]: cd bookdata/
|
||
|
|
/home/jdhunter/py4science/book/bookdata
|
||
|
|
|
||
|
|
In [2]: from pylab import *
|
||
|
|
|
||
|
|
In [2]: ion()
|
||
|
|
|
||
|
|
In [3]: im = imread('stinkbug.png')
|
||
|
|
|
||
|
|
@savefig mystinkbug.png width=4in
|
||
|
|
In [4]: imshow(im)
|
||
|
|
Out[4]: <matplotlib.image.AxesImage object at 0x39ea850>
|
||
|
|
|
||
|
|
""",
|
||
|
|
r"""
|
||
|
|
|
||
|
|
In [1]: x = 'hello world'
|
||
|
|
|
||
|
|
# string methods can be
|
||
|
|
# used to alter the string
|
||
|
|
@doctest
|
||
|
|
In [2]: x.upper()
|
||
|
|
Out[2]: 'HELLO WORLD'
|
||
|
|
|
||
|
|
@verbatim
|
||
|
|
In [3]: x.st<TAB>
|
||
|
|
x.startswith x.strip
|
||
|
|
""",
|
||
|
|
r"""
|
||
|
|
|
||
|
|
In [130]: url = 'http://ichart.finance.yahoo.com/table.csv?s=CROX\
|
||
|
|
.....: &d=9&e=22&f=2009&g=d&a=1&br=8&c=2006&ignore=.csv'
|
||
|
|
|
||
|
|
In [131]: print url.split('&')
|
||
|
|
['http://ichart.finance.yahoo.com/table.csv?s=CROX', 'd=9', 'e=22', 'f=2009', 'g=d', 'a=1', 'b=8', 'c=2006', 'ignore=.csv']
|
||
|
|
|
||
|
|
In [60]: import urllib
|
||
|
|
|
||
|
|
""",
|
||
|
|
r"""\
|
||
|
|
|
||
|
|
In [133]: import numpy.random
|
||
|
|
|
||
|
|
@suppress
|
||
|
|
In [134]: numpy.random.seed(2358)
|
||
|
|
|
||
|
|
@doctest
|
||
|
|
In [135]: numpy.random.rand(10,2)
|
||
|
|
Out[135]:
|
||
|
|
array([[ 0.64524308, 0.59943846],
|
||
|
|
[ 0.47102322, 0.8715456 ],
|
||
|
|
[ 0.29370834, 0.74776844],
|
||
|
|
[ 0.99539577, 0.1313423 ],
|
||
|
|
[ 0.16250302, 0.21103583],
|
||
|
|
[ 0.81626524, 0.1312433 ],
|
||
|
|
[ 0.67338089, 0.72302393],
|
||
|
|
[ 0.7566368 , 0.07033696],
|
||
|
|
[ 0.22591016, 0.77731835],
|
||
|
|
[ 0.0072729 , 0.34273127]])
|
||
|
|
|
||
|
|
""",
|
||
|
|
|
||
|
|
r"""
|
||
|
|
In [106]: print x
|
||
|
|
jdh
|
||
|
|
|
||
|
|
In [109]: for i in range(10):
|
||
|
|
.....: print i
|
||
|
|
.....:
|
||
|
|
.....:
|
||
|
|
0
|
||
|
|
1
|
||
|
|
2
|
||
|
|
3
|
||
|
|
4
|
||
|
|
5
|
||
|
|
6
|
||
|
|
7
|
||
|
|
8
|
||
|
|
9
|
||
|
|
""",
|
||
|
|
|
||
|
|
r"""
|
||
|
|
|
||
|
|
In [144]: from pylab import *
|
||
|
|
|
||
|
|
In [145]: ion()
|
||
|
|
|
||
|
|
# use a semicolon to suppress the output
|
||
|
|
@savefig test_hist.png width=4in
|
||
|
|
In [151]: hist(np.random.randn(10000), 100);
|
||
|
|
|
||
|
|
|
||
|
|
@savefig test_plot.png width=4in
|
||
|
|
In [151]: plot(np.random.randn(10000), 'o');
|
||
|
|
""",
|
||
|
|
|
||
|
|
r"""
|
||
|
|
# use a semicolon to suppress the output
|
||
|
|
In [151]: plt.clf()
|
||
|
|
|
||
|
|
@savefig plot_simple.png width=4in
|
||
|
|
In [151]: plot([1,2,3])
|
||
|
|
|
||
|
|
@savefig hist_simple.png width=4in
|
||
|
|
In [151]: hist(np.random.randn(10000), 100);
|
||
|
|
|
||
|
|
""",
|
||
|
|
r"""
|
||
|
|
# update the current fig
|
||
|
|
In [151]: ylabel('number')
|
||
|
|
|
||
|
|
In [152]: title('normal distribution')
|
||
|
|
|
||
|
|
|
||
|
|
@savefig hist_with_text.png
|
||
|
|
In [153]: grid(True)
|
||
|
|
|
||
|
|
@doctest float
|
||
|
|
In [154]: 0.1 + 0.2
|
||
|
|
Out[154]: 0.3
|
||
|
|
|
||
|
|
@doctest float
|
||
|
|
In [155]: np.arange(16).reshape(4,4)
|
||
|
|
Out[155]:
|
||
|
|
array([[ 0, 1, 2, 3],
|
||
|
|
[ 4, 5, 6, 7],
|
||
|
|
[ 8, 9, 10, 11],
|
||
|
|
[12, 13, 14, 15]])
|
||
|
|
|
||
|
|
In [1]: x = np.arange(16, dtype=float).reshape(4,4)
|
||
|
|
|
||
|
|
In [2]: x[0,0] = np.inf
|
||
|
|
|
||
|
|
In [3]: x[0,1] = np.nan
|
||
|
|
|
||
|
|
@doctest float
|
||
|
|
In [4]: x
|
||
|
|
Out[4]:
|
||
|
|
array([[ inf, nan, 2., 3.],
|
||
|
|
[ 4., 5., 6., 7.],
|
||
|
|
[ 8., 9., 10., 11.],
|
||
|
|
[ 12., 13., 14., 15.]])
|
||
|
|
|
||
|
|
|
||
|
|
""",
|
||
|
|
]
|
||
|
|
# skip local-file depending first example:
|
||
|
|
examples = examples[1:]
|
||
|
|
|
||
|
|
#ipython_directive.DEBUG = True # dbg
|
||
|
|
#options = dict(suppress=True) # dbg
|
||
|
|
options = {}
|
||
|
|
for example in examples:
|
||
|
|
content = example.split('\n')
|
||
|
|
IPythonDirective('debug', arguments=None, options=options,
|
||
|
|
content=content, lineno=0,
|
||
|
|
content_offset=None, block_text=None,
|
||
|
|
state=None, state_machine=None,
|
||
|
|
)
|
||
|
|
|
||
|
|
# Run test suite as a script
|
||
|
|
if __name__=='__main__':
|
||
|
|
if not os.path.isdir('_static'):
|
||
|
|
os.mkdir('_static')
|
||
|
|
test()
|
||
|
|
print('All OK? Check figures in _static/')
|